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Sample GSM2668160

Query DataSets for GSM2668160

Status

Public on Nov 28, 2017

Title

male_naive_neurons_2

Sample type

SRA

Source name

FACSed DRG neurons

Organism

Mus musculus

Characteristics

cell type: DRG neurons
strain: AdvGFP, gensat.org: STOCK Tg(Avil-EGFP)QD84Gsat/Mmucd
Sex: male
injury condition: naïve
estrus identification: no
contaminant: satellite glial cells

Extracted molecule

total RNA

Extraction protocol

RNA extractions were performed in a single, gender-matched batch using a Qiagen RNeasy micokit, following manufacturer’s protocols with some minor modifications. RNA quality was assessed using an Agilent Bioanalyser PicoChiP (for RIN values of sequencing samples see Supplementary Table 6).
RNA was sent for batch-controlled library preparation (SMARTer Ultra Low Input HV kit, 634820, Clontech) and sequencing at the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics at Oxford University. After amplification, samples were multiplexed in replicate flow cells on an Illumina HiSeq4500 platform to yield 75 bp reads of at least 25 M read depth.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Description

S210_male
Supplementary Table 1 (cufflinks), Supplementary Table 3 (deseq2), Supplementary Table 6 (QC)

Data processing

alignment using STAR to mm10 (standard parameters, except with --outFilterMultimapNmax 1)
merging of bam files across lanes using samtools
cufflinks for expression level determination (including fragment bias, length and multi-read corrections)
cufflinks expression cut-off deemed mathematically and biologically appropriate: FPKM >= 1
Deseq2 for differential expression level analysis (standard parameters)
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary Table 1: cufflinks-derived FPKM values for FACSed naïve DRG neurons with & without expression cut-off
Supplementary_files_format_and_content: Supplementary Table 2: cufflinks-derived FPKM values for MACSed DRG neurons after PSNL with and without expression cut-off
Supplementary_files_format_and_content: Supplementary Table 3: DESeq2 comparing male vs. female DRG neurons
Supplementary_files_format_and_content: Supplementary Table 6: RNA RIN values and alignment stats

Submission date

Jun 14, 2017

Last update date

May 15, 2019

Contact name

Franziska Denk

Organization name

King's College London

Street address

Guy's Campus

City

London